A wave field in a wave basin inevitably has spatial variation due to the wave’s cylindrical propagation property. Therefore, we aimed to develop an optimization method for the control of wave-makers to produce a spatially uniform wave field in a specified test zone inside a wave basin with an arbitrary arrangement of wave-makers. The optimization is based on the simulated annealing algorithm, a method for finding a globally optimal solution, which was combined with a numerical wave basin based on linear wave-maker theory. A wave generation experiment was performed in the actual sea model basin (80 m long, 40 m wide, and 4.5 m deep) at the National Maritime Research Institute to validate the proposed optimization method. A case study was conducted with a long-crested regular-wave with a wave height of 10 cm, wavelength of 4.0 m, and wave direction of 180 degrees, which corresponds to the longitudinal direction of the wave basin. A 40-m × 14-m test zone was set in the middle of the wave basin. The experimental results with and without the proposed optimization were compared, which confirmed that the spatial uniformity of the wave field was improved, and the coefficient of variation for the wave height in the test zone decreased from 0.127 to 0.029.